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4.4 years ago
linnet.roque6
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10
What is an OTU? operational taxonomic unit, but what is it for? what does it mean? Thanks!
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4.4 years ago
fawazfebin
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100
In metagenomics, OTU or Operatinal Taxonomic Unit is used to classify bacteria based on sequence similarity of the 16S marker gene. An OTU consists of a group of bacteria whose 16S marker gene shows a sequence identity of 97 percent and above. It is used to classify bacteria at the genus level.
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I understand your answer, it is good formulated. But it can be misleading for someone that does not know what a "OTU" is yet.
OTU or Operatinal Taxonomic Unit is used to classify bacteria
No, not only bacteria also eukaryotes
An OTU consists of a group of bacteria whose 16S marker gene
Same as above, and there are many other markers (COI, ITS, 18S, 12S etc.)
of 97 percent and above
This is not true ("anymore") just a identity percentage is not enough anymore. I know they did this in the early days. But it is proven that 97% might work for one family but not for the other.
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4.4 years ago
Joe
21k
In addition to the technical definition above, a more 'conceptual' definition is that an OTU is just a way of saying:
"This cluster of things is the same, and different from that cluster of things"
without having to assign a more 'meaningful' moniker to it (like a specific species name etc.) This is why it has the suitably vague term "operating taxonomic unit", to mean these are just arbitrary labels you assign/bins you put things in almost as a placeholder.
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Both answers bellow are correct, but incomplete. The Wikipedia page about operational taxonomic units is very short, but offers a bit of history about this term: it was introduced in the context of numerical taxonomy, and it a pragmatic approach to classify groups of organisms based on similarity of traits - originally, morphological traits. OTU was then picked by ecologists, as it allowed study of communities even when they are poorly characterized taxonomically. From there, it migrated to mOTU, or molecular OTU, when DNA barcoding started to be used as a proxy to classification, then people got lazy and dropped the "molecular" from the mOTU.
All this to say the concept of OTUs can be applied to any group of organisms, at any taxonomic level, using any arbitrarily defined set of traits. It just so happens nowadays its most common usage is for bacterial molecular markers.